1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
|
Source: any2fasta
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Build-Depends: debhelper-compat (= 13)
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/any2fasta
Vcs-Git: https://salsa.debian.org/med-team/any2fasta.git
Homepage: https://github.com/tseemann/any2fasta
Rules-Requires-Root: no
Package: any2fasta
Architecture: all
Depends: ${perl:Depends},
${misc:Depends}
Multi-Arch: foreign
Description: convert various sequence formats to FASTA
Established tools like readseq and seqret from EMBOSS, both create mangled
IDs containing | or . characters, and there is no way to fix this behaviour.
This resultes in inconsitences between .gbk and .fna versions of files in
pipelines.
.
This script uses only core Perl modules, has no other dependencies like
Bioperl or Biopython, and runs very quickly.
.
It supports the following input formats:
.
1. Genbank flat file, typically .gb, .gbk, .gbff (starts with LOCUS)
2. EMBL flat file, typically .embl, (starts with ID)
3. GFF with sequence, typically .gff, .gff3 (starts with ##gff)
4. FASTA DNA, typically .fasta, .fa, .fna, .ffn (starts with >)
5. FASTQ DNA, typically .fastq, .fq (starts with @)
6. CLUSTAL alignments, typically .clw, .clu (starts with CLUSTAL or MUSCLE)
7. STOCKHOLM alignments, typically .sth (starts with # STOCKHOLM)
8. GFA assembly graph, typically .gfa (starts with ^[A-Z]\t)
.
Files may be compressed with:
.
1. gzip, typically .gz
2. bzip2, typically .bz2
3. zip, typically .zip
Package: any2fasta-examples
Architecture: all
Depends: ${misc:Depends}
Multi-Arch: foreign
Description: convert various sequence formats to FASTA (example data)
Established tools like readseq and seqret from EMBOSS, both create mangled
IDs containing | or . characters, and there is no way to fix this behaviour.
This resultes in inconsitences between .gbk and .fna versions of files in
pipelines.
.
This script uses only core Perl modules, has no other dependencies like
Bioperl or Biopython, and runs very quickly.
.
It supports the following input formats:
.
1. Genbank flat file, typically .gb, .gbk, .gbff (starts with LOCUS)
2. EMBL flat file, typically .embl, (starts with ID)
3. GFF with sequence, typically .gff, .gff3 (starts with ##gff)
4. FASTA DNA, typically .fasta, .fa, .fna, .ffn (starts with >)
5. FASTQ DNA, typically .fastq, .fq (starts with @)
6. CLUSTAL alignments, typically .clw, .clu (starts with CLUSTAL or MUSCLE)
7. STOCKHOLM alignments, typically .sth (starts with # STOCKHOLM)
8. GFA assembly graph, typically .gfa (starts with ^[A-Z]\t)
.
Files may be compressed with:
.
1. gzip, typically .gz
2. bzip2, typically .bz2
3. zip, typically .zip
.
This package contains some example data for testing.
|
